4NYF

HIV integrase in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report



Literature

Discovery of BI 224436, a Noncatalytic Site Integrase Inhibitor (NCINI) of HIV-1.

Fader, L.D.Malenfant, E.Parisien, M.Carson, R.Bilodeau, F.Landry, S.Pesant, M.Brochu, C.Morin, S.Chabot, C.Halmos, T.Bousquet, Y.Bailey, M.D.Kawai, S.H.Coulombe, R.LaPlante, S.Jakalian, A.Bhardwaj, P.K.Wernic, D.Schroeder, P.Amad, M.Edwards, P.Garneau, M.Duan, J.Cordingley, M.Bethell, R.Mason, S.W.Bos, M.Bonneau, P.Poupart, M.A.Faucher, A.M.Simoneau, B.Fenwick, C.Yoakim, C.Tsantrizos, Y.

(2014) ACS Med Chem Lett 5: 422-427

  • DOI: 10.1021/ml500002n
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • An assay recapitulating the 3' processing activity of HIV-1 integrase (IN) was used to screen the Boehringer Ingelheim compound collection. Hit-to-lead and lead optimization beginning with compound 1 established the importance of the C3 and C4 substi ...

    An assay recapitulating the 3' processing activity of HIV-1 integrase (IN) was used to screen the Boehringer Ingelheim compound collection. Hit-to-lead and lead optimization beginning with compound 1 established the importance of the C3 and C4 substituent to antiviral potency against viruses with different aa124/aa125 variants of IN. The importance of the C7 position on the serum shifted potency was established. Introduction of a quinoline substituent at the C4 position provided a balance of potency and metabolic stability. Combination of these findings ultimately led to the discovery of compound 26 (BI 224436), the first NCINI to advance into a phase Ia clinical trial.


    Organizational Affiliation

    Research and Development, Boehringer Ingelheim (Canada) Ltd. , 2100 Cunard Street, Laval, Québec H7S 2G5, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrase
A, B
168Human immunodeficiency virus type 1 lw12.3 isolateMutation(s): 4 
Gene Names: gag-pol
EC: 2.7.7 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 3.1 (UniProt)
Find proteins for P0C6F2 (Human immunodeficiency virus type 1 group M subtype B (isolate LW123))
Go to UniProtKB:  P0C6F2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4BI
Query on 4BI

Download CCD File 
A
(2S)-tert-butoxy[4-(4-chlorophenyl)-2-methylquinolin-3-yl]ethanoic acid
C22 H22 Cl N O3
BCLKGXWEVQRUHG-FQEVSTJZSA-N
 Ligand Interaction
CD
Query on CD

Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4BIKd:  49   nM  Binding MOAD
4BIKd:  49   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.77α = 90
b = 62.45β = 90
c = 81.32γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
CNXphasing
CNXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release